Nope, you're alright. Most opensource parsers doesn't handle segwit and are not able to parse blocks included in recent blk files. I had to build my own parser to be able to parse files after these ones too. 
If I were you, I'd write a script to run everything from the bitcoin daemon or the bitcoin-qt cli (or whatever client you're running) and then you don't have to keep updating it.
Also, if you're going to run it in a separate script (away from bitcoin core) that is going to read the data, put the blockchain in a different folder.